Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014865.1 Corchorus olitorius cultivar O-4 contig14898, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 8364
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:1271 original size:22 final size:24

Alignment explanation


    Indices: 1236--1289  Score: 60
    Period size: 22  Copynumber: 2.3  Consensus size: 24

       1226 ATAAATGTTG

                            *      *
       1236 CTGATAA-TCTTCT-CTTTTATCT
          1 CTGATAATTCTTCTCCATTTATCA

                                    
       1258 CTGATAATTC-TCTCCATTTATCA
          1 CTGATAATTCTTCTCCATTTATCA

                     
       1281 CTTGATAAT
          1 C-TGATAAT

       1290 ATCTAGCCAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
  22   10  0.37
  23   10  0.37
  24    7  0.26

ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48


Consensus pattern (24 bp):   
CTGATAATTCTTCTCCATTTATCA

Found at i:5485 original size:30 final size:30

Alignment explanation


    Indices: 5444--6041  Score: 750
    Period size: 30  Copynumber: 19.8  Consensus size: 30

       5434 TGAAAGGTAA

                            *             *
       5444 ATCATGACAACTTCTGTTGTCAATTG-AATT
          1 ATCATGACAACTTCTGGTGTCAATTGCAA-G

                  *                       
       5474 ATCATGGCAACTTCTGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *                            
       5504 AGCATGACAACTTCTGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *           *               *
       5534 AGCATGACAACTTATGGTGTCAATTGCAAC
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                                          *
       5564 AGT-ATGACAACTTCTGGTGTCAATTGCAAC
          1 A-TCATGACAACTTCTGGTGTCAATTGCAAG

             *             *            * 
       5594 AGCATGACAACTTCTAGTGTCAATTGCAGG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *        *            *    * 
       5624 AGCATGACAAGTTCTGGTGTCAACTGCAGG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *            **              
       5654 AGCATGACAACTTCAAGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                                           
       5684 ATCATTGACAACTTCTGGTGTCAATTGCAAG
          1 ATCA-TGACAACTTCTGGTGTCAATTGCAAG

            **                            
       5715 GCCATGACAACTTCTGGTGTCAATTGCAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *           *            *   
       5745 ACCATGACAACTTATGGTGTCAATTGTAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *                         *   
       5775 ACCATTGACAACTTCTGGTGTCAATTGTAAG
          1 ATCA-TGACAACTTCTGGTGTCAATTGCAAG

                                      *   
       5806 ATCATGACAACTTCTGGTGTCAATTGTAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                                       *   
       5836 ATCATTGACAACTTCTGGTGTCAATTGTAAG
          1 ATCA-TGACAACTTCTGGTGTCAATTGCAAG

             *                        *   
       5867 ACCATGACAACTTCTGGTGTCAATTGTAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *                    *   *   
       5897 ACCATGACAACTTCTGGTGTCATTTGTAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *                    *   *   
       5927 ACCATGACAACTTCTGGTGTCATTTGTAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                *                 *   *   
       5957 ATCAAGACAACTTCTGGTGTCATTTGTAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

             *                    *   *   
       5987 ACCATGACAACTTCTGGTGTCATTTGTAAG
          1 ATCATGACAACTTCTGGTGTCAATTGCAAG

                  *                  
       6017 ATCATTCACAACTTCTGGTGTCAAT
          1 ATCA-TGACAACTTCTGGTGTCAAT

       6042 ATATATTAGC


Statistics
Matches: 521,  Mismatches: 40, Indels: 13
        0.91            0.07        0.02

Matches are distributed among these distances:
  30  418  0.80
  31  103  0.20

ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31


Consensus pattern (30 bp):   
ATCATGACAACTTCTGGTGTCAATTGCAAG

Found at i:7106 original size:23 final size:23

Alignment explanation


    Indices: 7065--7118  Score: 65
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       7055 ATAAATGTTG

                           *      *
       7065 CTGATAA-TCTTCTCTTTTATCT
          1 CTGATAATTCTTCTCATTTATCA

                        *          
       7087 CTGATAATTCTTTTCATTTATCA
          1 CTGATAATTCTTCTCATTTATCA

                     
       7110 CTTGATAAT
          1 C-TGATAAT

       7119 ATCTAGCCAG


Statistics
Matches: 27,  Mismatches: 3, Indels: 2
        0.84            0.09        0.06

Matches are distributed among these distances:
  22    7  0.26
  23   13  0.48
  24    7  0.26

ACGTcount: A:0.24, C:0.19, G:0.06, T:0.52


Consensus pattern (23 bp):   
CTGATAATTCTTCTCATTTATCA

Found at i:7371 original size:16 final size:16

Alignment explanation


    Indices: 7331--7380  Score: 64
    Period size: 16  Copynumber: 3.1  Consensus size: 16

       7321 TAAATTCAAA

                            
       7331 TTATTTCGGGTTCGGG
          1 TTATTTCGGGTTCGGG

            *  **           
       7347 CTACCTCGGGTTCGGG
          1 TTATTTCGGGTTCGGG

                     *      
       7363 TTATTTCGGATTCGGG
          1 TTATTTCGGGTTCGGG

              
       7379 TT
          1 TT

       7381 TGGGACGTTG


Statistics
Matches: 27,  Mismatches: 7, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  16   27  1.00

ACGTcount: A:0.08, C:0.18, G:0.34, T:0.40


Consensus pattern (16 bp):   
TTATTTCGGGTTCGGG
Done.